AMBER Archive (2008)

Subject: Re: AMBER: Amber GB problems on PMEMD !!

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Thu Sep 25 2008 - 10:12:59 CDT

Hi,
> I am sorry. I did not mean to indicate that there is a problem with pmemd. I just wanted to tell that I was using pmemd for all these tests.
>
> Just to add an other note to my previous email: My tests on Villin head and GB1 (PDB id : nug2) using mbondi and igb7 seem quite good but bondi and igb=7 seem too-solvated and the protein seem to be falling apart (this is 1 ns of MD of the native state)
>
> Is there a publication which suggests the best gb method in Amber ?
>
...I guess there's no "best" gb method (yet). You could study what
(parameters/GB model/simulation method) others used to obeserve folding of
a protein
(see http://pubs.acs.org/cgi-bin/abstract.cgi/jacsat/2002/124/i38/abs/ja0273851.html)

A more direct answer to your question might be found here:
http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/2008/112/i22/abs/jp800282x.html

good luck
Andreas
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